Question: How to convert old entrez id to updated-entrez id in R?
5
gravatar for agicict
2.8 years ago by
agicict130
Korea, Republic Of
agicict130 wrote:

Hi.

Like other identifiers, entrez ids are also change as time goes by.

I used two library, 'org.Hs.eg.db' and 'annotate', to convert entrez ids into gene symbols.

Some of entrez ids were not changed because of updates.

Take entrez id 164022 as an example,

library(org.Hs.eg.db);library(annotate)
getSYMBOL('164022',data = 'org.Hs.eg')

164022 
NA

If you search the entrez id at NCBI, it says that 164022 was replaced with 653505.

(See. http://www.ncbi.nlm.nih.gov/gene/?term=164022)

Therefore, you should use the newest entrez id to get its gene symbol.

getSYMBOL('653505',data = 'org.Hs.eg')
   653505 
"PPIAL4A"

There are about two hundreds entrez ids whose symbol-matching failed.

As manual searching requires huge time, I need a solution.

How to update old entrez ids into newest entrez id?

Is there a function or library for this?

entrez id update R • 1.3k views
ADD COMMENTlink modified 2.8 years ago by Giovanni M Dall'Olio26k • written 2.8 years ago by agicict130
7
gravatar for Giovanni M Dall'Olio
2.8 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

This is a very good question.

You may try with the mygene.info service:

$: curl mygene.info/v2/gene/164022?fields=entrezgene
{
_id: "653505",
entrezgene: 653505
}

Remove the "fields" parameter to get more information.

For more documentation on mygene.info, check http://mygene.info/v2/api#MyGene.info-gene-annotation-services-GET-Gene-annotation-service

ADD COMMENTlink written 2.8 years ago by Giovanni M Dall'Olio26k
1

Thank you. I used getURL function of RCurl to retrieve the information from the site.

ADD REPLYlink written 2.8 years ago by agicict130
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